Hi Doug,


No worries at all! Thanks for your input, I will go ahead and do that. 

In addition to calculating  the number of WM hyperintensity voxels in each adjacent cortical label, I was also interested in creating a figure depicting the potential significant correlations between regional WM hyperintensity burden and cortical thinning. Is there a way to statistically compare two surface maps (i.e., the *h.thickness surface map and the projected-to-the-cortex WM hyperintensity map) to come up with such a figure?


Thanks again!

Best,

panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgreve@mgh.harvard.edu>
Sent: Thursday, May 31, 2018 2:54:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Regional comparisons between cortical thickness and white matter hyperintensity
 

sorry, fell through the cracks!

The easier way to do this is to use the wmparc.mgz. This is a segmentation where the WM is labeled based on the adjacent cortical label. You can run something like

mri_segstats --i wmhyper.mgz --seg wmparc.mgz --ctab-default --accumulate --sum sum.dat

The sum.dat will have the number of voxels of wmh in each ROI. There will be a lot of ROIs in the sum.dat, so you'll have to filter through them


On 5/31/18 11:30 AM, Fotiadis, Panagiotis wrote:

Hi all,


Just wanted to re-circulate this, just in case someone had some input!


Thanks,

Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fotiadis, Panagiotis <PFOTIADIS@mgh.harvard.edu>
Sent: Friday, May 25, 2018 10:49:10 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Regional comparisons between cortical thickness and white matter hyperintensity
 

Hello,


I'm interested in looking into the association of cortical thickness and white matter hyperintensity from a regional perspective. Specifically, I would like to create a figure that depicts in which ROIs does cortical thinning correlate significantly with increased white matter hyperintensity volume of the underlying white matter (not just the overall white matter hyperintensity). I have created binary masks of the white matter hyperintensity burden on each patient, and I was planning on projecting them into each respective cortex. However, I didn't know what the next step should be. I was thinking about the group analysis pipeline but didn't know whether it was applicable, as I don't want to just adjust for global white matter hyperintensity volume.

Thanks in advance for any help!


Best,

Panos


Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869


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